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PDBsum entry 2cjw

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G-protein PDB id
2cjw
Jmol
Contents
Protein chains
178 a.a.
173 a.a.
Ligands
GDP ×2
Metals
_MG ×2
Waters ×127

References listed in PDB file
Key reference
Title Biochemical and structural characterization of the gem gtpase.
Authors A.Splingard, J.Ménétrey, M.Perderiset, J.Cicolari, K.Regazzoni, F.Hamoudi, L.Cabanié, A.El marjou, A.Wells, A.Houdusse, J.De gunzburg.
Ref. J Biol Chem, 2007, 282, 1905-1915. [DOI no: 10.1074/jbc.M604363200]
PubMed id 17107948
Abstract
RGK proteins, encompassing Rad, Gem, Rem1, and Rem2, constitute an intriguing branch of the Ras superfamily; their expression is regulated at the transcription level, they exhibit atypical nucleotide binding motifs, and they carry both large N- and C-terminal extensions. Biochemical and structural studies are required to better understand how such proteins function. Here, we report the first structure for a RGK protein: the crystal structure of a truncated form of the human Gem protein (G domain plus the first part of the C-terminal extension) in complex with Mg.GDP at 2.1 A resolution. It reveals that the G-domain fold and Mg.GDP binding site of Gem are similar to those found for other Ras family GTPases. The first part of the C-terminal extension adopts an alpha-helical conformation that extends along the alpha5 helix and interacts with the tip of the interswitch. Biochemical studies show that the affinities of Gem for GDP and GTP are considerably lower (micromolar range) compared with H-Ras, independent of the presence or absence of N- and C-terminal extensions, whereas its GTPase activity is higher than that of H-Ras and regulated by both extensions. We show how the bulky DXWEX motif, characteristic of the switch II of RGK proteins, affects the conformation of switch I and the phosphate-binding site. Altogether, our data reveal that Gem is a bona fide GTPase that exhibits striking structural and biochemical features that should impact its regulation and cellular activities.
Figure 4.
Crystal structure of GDP-bound Gem-ΔNΔCaM. A, an overall view of Gem-ΔNΔCaM-GDP is shown with switch I in green, the interswitch in yellow, switch II in pink, and the C-terminal helix in blue. Note that both conformations of switch I and II are shown superposed in dark for molecule A and in bright for molecule B. B, the scheme of Mg·GDP interactions is given for molecule A with distances (see supplemental Table S1 for distances in molecule B). An inset of the magnesium coordination sphere is shown separately for clarity. C, close view of the C-terminal helix (blue) and its interaction with the interswitch (yellow) and the α5 helix (white) with secondary structure shown as coils. Hydrogen bonds are indicated by dashed lines. Note that for clarity, the orientation is not strictly conserved with the overall view (A). D, close view of the DMWEN motif in switch II (pink). The side chain of Glu^134 from molecule A is shown as transparent, indicating its partial occupancy. Orientation with the overall view is conserved.
Figure 5.
Comparison of the switch regions of GemΔNΔCaM-GDP with H-Ras-GDP/GTP. A, the H-Ras-GDP (Protein Data Bank code 4Q21; transparent light blue) and H-Ras-GTP (Protein Data Bank code 5P21; transparent dark blue) switch I-interswitch-switch II regions are shown superposed on the GemΔNΔCaM-GDP structure (same colors as in Fig. 4) for comparison. B, close view of A with overall structure shown as coils and the C-terminal part of switch II deleted for clarity. The first residues from the DMWEN and DTAGQ motifs in Gem and H-Ras, respectively, are shown in ball-and-stick representations for comparison. Note the divergent backbone trace and side chain directions between Gem and H-Ras after the Asp^131/Asp^57 residues and the position of Met^132 that shortens the β2 strand, pushing switch I away from the nucleotide binding site in Gem when compared with H-Ras.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 1905-1915) copyright 2007.
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